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Citations per year

Number of citations per year for the bioinformatics software tool BASH
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Protocols

BASH specifications

Information


Unique identifier OMICS_14400
Name BASH
Alternative name BeadArray Subversion of Harshlight
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.30.0
Stability Stable
Requirements
AnnotationDbi, limma, methods, IRanges, GenomicRanges, BiocStyle, stats4, ggplot2, affy, knitr, reshape2, illuminaio, vsn, beadarrayExampleData, R(>=2.13.0), TxDb.Hsapiens.UCSC.hg19.knownGene, hwriter, Biobase(>=2.17.8), lumi, BiocGenerics(>=0.3.2), BeadDataPackR, illuminaHumanv3.db, gridExtra, ggbio, Nozzle.R1
Maintained Yes

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Maintainer


  • person_outline Andy Lynch

Publication for BeadArray Subversion of Harshlight

BASH citations

 (32)
library_books

Dynamics of DNA methylomes underlie oyster development

2017
PLoS Genet
PMCID: 5481141
PMID: 28594821
DOI: 10.1371/journal.pgen.1006807

[…] Data were analysed using a using a combination of dedicated R (bioconductor.org) and bash script as well as in-house R, bash, TiCL and PERL scripts. Data source files (NCBI project PRJNA324546) and scripts used for analyses are publicly available (github.com/BOREA-UNICAEN/MeDIPSeq-Dev […]

call_split

p120 catenin prevents multinucleation through control of MKLP1 dependent RhoA activity during cytokinesis

2016
Nat Commun
PMCID: 5192218
PMID: 28004812
DOI: 10.1038/ncomms13874
call_split See protocol

[…] g thresholds based on the variability of each sample and their proportion of normal contamination. RNA analysis was performed using Illumina HT-12 v3 platform and analysed with the beadarray package. BASH algorithm was employed to correct for spatial artefacts. Bead-level data was summarized and a selection of suitable probes based on their quality was done using the re-annotation of the Illumina […]

library_books

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle

2016
Sci Rep
PMCID: 5120318
PMID: 27876851
DOI: 10.1038/srep37536

[…] Data analysis was conducted in a UNIX environment or Microsoft Excel 2007 using standard commands. Bioinformatic scripts required to facilitate data analysis were designed using bash, GNU coreutils, Perl, and Python. […]

library_books

Stratification and therapeutic potential of PML in metastatic breast cancer

2016
Nat Commun
PMCID: 4999521
PMID: 27553708
DOI: 10.1038/ncomms12595

[…] is data set patients, RNA was extracted from 1,980 tumours as described. RNA hybridizations were performed using Illumina HT-12 v3 platform and analysed using the bioconductor bead array package. The BASH algorithm was applied to correct for spatial artefacts in the arrays. Bead-level data were summarized and re-annotated as described in ref. . Log-intensity values for PML expression were scaled t […]

library_books

Reliable gene expression profiling of formalin fixed paraffin embedded breast cancer tissue (FFPE) using cDNA mediated annealing, extension, selection, and ligation whole genome (DASL WG) assay

2016
BMC Med Genomics
PMCID: 4992321
PMID: 27542606
DOI: 10.1186/s12920-016-0215-4

[…] Illumina microarray experiments were analysed using BeadStudio® software (Illumina, San Diego) and R (version 2.6.0) [].During this analysis, image files were loaded using the BeadArray package. The BASH algorithm was used to remove spatial artifacts []. The algorithm generates a grid of neighbours for each bead and identifies three types of defects: compact, diffuse (regions that contain more ou […]

library_books

Identification of host transcriptional networks showing concentration dependent regulation by HPV16 E6 and E7 proteins in basal cervical squamous epithelial cells

2016
Sci Rep
PMCID: 4960560
PMID: 27457222
DOI: 10.1038/srep29832

[…] with the Illumina Human v4 annotation. The bead-level data were assessed for integrity at multiple levels. Raw image quality was assessed visually, by viewing image plots, and numerically, using the BASH algorithm, and weights assigned to each probe.The data were log-transformed and probes summarized to provide probe-set data for downstream analysis. Quantile normalisation was applied in order to […]


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BASH institution(s)
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
BASH funding source(s)
This work was funded by The University of Cambridge, Cancer Research UK; Hutchison Whampoa Limited.

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